1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
|
/* Copyright (C) 2001-2003 Damir Zucic */
/*=============================================================================
select_element.c
Purpose:
Try to interpret the selection string as the request to select the
the specified chemical element. There are three selection modes:
0 = overwrite, 1 = restrict, 2 = expand the previous selection.
This function expects that the second token in the command line is
the keyword ELEMENT (short version is ELE). If it is not found,
the function will return negative value.
Input:
(1) Pointer to MolComplexS structure, with macromol. complexes.
(2) Number of macromolecular complexes.
(3) The selection string.
(4) Selection mode index (0 = overwr., 1 = restrict, 2 = expand).
Output:
(1) The flag selectedF will be equal to one for selected atoms and
equal to zero for all other atoms.
(2) Return value.
Return value:
(1) The number of selected atoms, if selection is done in this
function.
(2) Negative value on failure.
Notes:
(1) The standard chemical symbols should be used to specify the
chemical elements. In addition to well known elements, two
imaginary elements were added: jellium (J) and quarkonium (Q).
Jellium is inert - it is never involved in chemical bonds.
Quarkonium binds to neighboring atoms in the list of Q atoms,
i.e. to quarkonium atoms which have adjacent atomic serial
numbers. The actual distance between quarkonium atoms is not
important. Quarkonium may be used for polygonal lines in 3D.
J and Q were introduced to adapt garlic for visualization of
medical data.
========includes:============================================================*/
#include <stdio.h>
#include <string.h>
#include <X11/Xlib.h>
#include <X11/Xutil.h>
#include <X11/Xos.h>
#include <X11/Xatom.h>
#include "defines.h"
#include "typedefs.h"
/*======function prototypes:=================================================*/
char *ExtractToken_ (char *, int, char *, char *);
/*======select the specified chemical element:===============================*/
long SelectElement_ (MolComplexS *mol_complexSP, int mol_complexesN,
char *stringP, int selection_modeI)
{
long selected_atomsN = 0;
char *remainderP;
char tokenA[STRINGSIZE];
int mol_complexI;
MolComplexS *curr_mol_complexSP;
size_t atomsN, atomI;
AtomS *curr_atomSP;
char *P;
char chemical_symbolA[20];
int elementF;
/* Extract the first token and check it (look for substring ELE): */
remainderP = ExtractToken_ (tokenA, STRINGSIZE, stringP, " \t\n");
if (!strstr (tokenA, "ELE")) return (long) -1;
/* Try to extract one more token (chemical symbol expected): */
remainderP = ExtractToken_ (tokenA, STRINGSIZE, remainderP, " \t\n");
if (!remainderP) return (long) -2;
/* Check every macromolecular complex: */
for (mol_complexI = 0; mol_complexI < mol_complexesN; mol_complexI++)
{
/* Pointer to the current macromolecular complex: */
curr_mol_complexSP = mol_complexSP + mol_complexI;
/* Check is the current macromolecular complex caught: */
if (curr_mol_complexSP->catchF == 0) continue;
/* Number of atoms in a macromolecular complex: */
atomsN = curr_mol_complexSP->atomsN;
/* Scan all atoms in the current complex: */
for (atomI = 0; atomI < atomsN; atomI++)
{
/* Pointer to the current atom: */
curr_atomSP = curr_mol_complexSP->atomSP + atomI;
/* Extract the chemical symbol of the current atom: */
P = curr_atomSP->raw_atomS.chemical_symbolA;
remainderP = ExtractToken_ (chemical_symbolA, 20, P, " \t");
if (!remainderP) continue;
/* Check the chemical symbol: */
elementF = 0;
if (strcmp (chemical_symbolA, tokenA) == 0) elementF = 1;
/* Set the selection flag for the current atom: */
switch (selection_modeI)
{
/* Overwrite the previous selection: */
case 0:
curr_atomSP->selectedF = elementF;
break;
/* Restrict the previous selection: */
case 1:
curr_atomSP->selectedF &= elementF;
break;
/* Expand the previous selection: */
case 2:
curr_atomSP->selectedF |= elementF;
break;
default:
;
}
/* Check the selection flag; increase */
/* the count if flag is equal to one: */
if (curr_atomSP->selectedF) selected_atomsN++;
}
/* Update the position_changedF (some atoms may have bad color): */
curr_mol_complexSP->position_changedF = 1;
}
/* Return the number of selected atoms: */
return selected_atomsN;
}
/*===========================================================================*/
|
